GLORIA

GEOMAR Library Ocean Research Information Access

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    Online Resource
    Online Resource
    Spandidos Publications ; 2017
    In:  Biomedical Reports Vol. 6, No. 1 ( 2017-01), p. 57-62
    In: Biomedical Reports, Spandidos Publications, Vol. 6, No. 1 ( 2017-01), p. 57-62
    Type of Medium: Online Resource
    ISSN: 2049-9434 , 2049-9442
    Language: English
    Publisher: Spandidos Publications
    Publication Date: 2017
    detail.hit.zdb_id: 2763624-0
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 2
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2021
    In:  Proceedings of the National Academy of Sciences Vol. 118, No. 6 ( 2021-02-09)
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 118, No. 6 ( 2021-02-09)
    Abstract: RNA polymerase II (Pol II) generally pauses at certain positions along gene bodies, thereby interrupting the transcription elongation process, which is often coupled with various important biological functions, such as precursor mRNA splicing and gene expression regulation. Characterizing the transcriptional elongation dynamics can thus help us understand many essential biological processes in eukaryotic cells. However, experimentally measuring Pol II elongation rates is generally time and resource consuming. We developed PEPMAN (polymerase II elongation pausing modeling through attention-based deep neural network), a deep learning-based model that accurately predicts Pol II pausing sites based on the native elongating transcript sequencing (NET-seq) data. Through fully taking advantage of the attention mechanism, PEPMAN is able to decipher important sequence features underlying Pol II pausing. More importantly, we demonstrated that the analyses of the PEPMAN-predicted results around various types of alternative splicing sites can provide useful clues into understanding the cotranscriptional splicing events. In addition, associating the PEPMAN prediction results with different epigenetic features can help reveal important factors related to the transcription elongation process. All these results demonstrated that PEPMAN can provide a useful and effective tool for modeling transcription elongation and understanding the related biological factors from available high-throughput sequencing data.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
    RVK:
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2021
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 3
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2023
    In:  Journal of Radioanalytical and Nuclear Chemistry Vol. 332, No. 9 ( 2023-09), p. 3827-3836
    In: Journal of Radioanalytical and Nuclear Chemistry, Springer Science and Business Media LLC, Vol. 332, No. 9 ( 2023-09), p. 3827-3836
    Type of Medium: Online Resource
    ISSN: 0236-5731 , 1588-2780
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2017242-4
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 4
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2021-06-03)
    Abstract: Despite decades of intensive search for compounds that modulate the activity of particular protein targets, a large proportion of the human kinome remains as yet undrugged. Effective approaches are therefore required to map the massive space of unexplored compound–kinase interactions for novel and potent activities. Here, we carry out a crowdsourced benchmarking of predictive algorithms for kinase inhibitor potencies across multiple kinase families tested on unpublished bioactivity data. We find the top-performing predictions are based on various models, including kernel learning, gradient boosting and deep learning, and their ensemble leads to a predictive accuracy exceeding that of single-dose kinase activity assays. We design experiments based on the model predictions and identify unexpected activities even for under-studied kinases, thereby accelerating experimental mapping efforts. The open-source prediction algorithms together with the bioactivities between 95 compounds and 295 kinases provide a resource for benchmarking prediction algorithms and for extending the druggable kinome.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2553671-0
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 5
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2021
    In:  Nature Communications Vol. 12, No. 1 ( 2021-09-15)
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 12, No. 1 ( 2021-09-15)
    Abstract: Peptide-protein interactions are involved in various fundamental cellular functions and their identification is crucial for designing efficacious peptide therapeutics. Recently, a number of computational methods have been developed to predict peptide-protein interactions. However, most of the existing prediction approaches heavily depend on high-resolution structure data. Here, we present a deep learning framework for multi-level peptide-protein interaction prediction, called CAMP, including binary peptide-protein interaction prediction and corresponding peptide binding residue identification. Comprehensive evaluation demonstrated that CAMP can successfully capture the binary interactions between peptides and proteins and identify the binding residues along the peptides involved in the interactions. In addition, CAMP outperformed other state-of-the-art methods on binary peptide-protein interaction prediction. CAMP can serve as a useful tool in peptide-protein interaction prediction and identification of important binding residues in the peptides, which can thus facilitate the peptide drug discovery process.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2553671-0
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 6
    Online Resource
    Online Resource
    Frontiers Media SA ; 2020
    In:  Frontiers in Pharmacology Vol. 11 ( 2020-2-28)
    In: Frontiers in Pharmacology, Frontiers Media SA, Vol. 11 ( 2020-2-28)
    Type of Medium: Online Resource
    ISSN: 1663-9812
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2020
    detail.hit.zdb_id: 2587355-6
    SSG: 15,3
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 7
    Online Resource
    Online Resource
    Royal Society of Chemistry (RSC) ; 2022
    In:  Digital Discovery Vol. 1, No. 3 ( 2022), p. 195-208
    In: Digital Discovery, Royal Society of Chemistry (RSC), Vol. 1, No. 3 ( 2022), p. 195-208
    Abstract: Computers can already be programmed for superhuman pattern recognition of images and text. For machines to discover novel molecules, they must first be trained to sort through the many characteristics of molecules and determine which properties should be retained, suppressed, or enhanced to optimize functions of interest. Machines need to be able to understand, read, write, and eventually create new molecules. Today, this creative process relies on deep generative models, which have gained popularity since powerful deep neural networks were introduced to generative model frameworks. In recent years, they have demonstrated excellent ability to model complex distribution of real-word data ( e.g. , images, audio, text, molecules, and biological sequences). Deep generative models can generate data beyond those provided in training samples, thus yielding an efficient and rapid tool for exploring the massive search space of high-dimensional data such as DNA/protein sequences and facilitating the design of biomolecules with desired functions. Here, we review the emerging field of deep generative models applied to peptide science. In particular, we discuss several popular deep generative model frameworks as well as their applications to generate peptides with various kinds of properties ( e.g. , antimicrobial, anticancer, cell penetration, etc ). We conclude our review with a discussion of current limitations and future perspectives in this emerging field.
    Type of Medium: Online Resource
    ISSN: 2635-098X
    Language: English
    Publisher: Royal Society of Chemistry (RSC)
    Publication Date: 2022
    detail.hit.zdb_id: 3142965-8
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 8
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2020
    In:  Bioinformatics Vol. 36, No. 9 ( 2020-05-01), p. 2872-2880
    In: Bioinformatics, Oxford University Press (OUP), Vol. 36, No. 9 ( 2020-05-01), p. 2872-2880
    Abstract: Quantitative structure–activity relationship (QSAR) and drug–target interaction (DTI) prediction are both commonly used in drug discovery. Collaboration among pharmaceutical institutions can lead to better performance in both QSAR and DTI prediction. However, the drug-related data privacy and intellectual property issues have become a noticeable hindrance for inter-institutional collaboration in drug discovery. Results We have developed two novel algorithms under secure multiparty computation (MPC), including QSARMPC and DTIMPC, which enable pharmaceutical institutions to achieve high-quality collaboration to advance drug discovery without divulging private drug-related information. QSARMPC, a neural network model under MPC, displays good scalability and performance and is feasible for privacy-preserving collaboration on large-scale QSAR prediction. DTIMPC integrates drug-related heterogeneous network data and accurately predicts novel DTIs, while keeping the drug information confidential. Under several experimental settings that reflect the situations in real drug discovery scenarios, we have demonstrated that DTIMPC possesses significant performance improvement over the baseline methods, generates novel DTI predictions with supporting evidence from the literature and shows the feasible scalability to handle growing DTI data. All these results indicate that QSARMPC and DTIMPC can provide practically useful tools for advancing privacy-preserving drug discovery. Availability and implementation The source codes of QSARMPC and DTIMPC are available on the GitHub: https://github.com/rongma6/QSARMPC_DTIMPC.git. Supplementary information Supplementary data are available at Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1367-4803 , 1367-4811
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1468345-3
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 9
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2019
    In:  Genomics, Proteomics & Bioinformatics Vol. 17, No. 5 ( 2019-10-01), p. 478-495
    In: Genomics, Proteomics & Bioinformatics, Oxford University Press (OUP), Vol. 17, No. 5 ( 2019-10-01), p. 478-495
    Abstract: Accurate identification of compound–protein interactions (CPIs) in silico may deepen our understanding of the underlying mechanisms of drug action and thus remarkably facilitate drug discovery and development. Conventional similarity- or docking-based computational methods for predicting CPIs rarely exploit latent features from currently available large-scale unlabeled compound and protein data and often limit their usage to relatively small-scale datasets. In the present study, we propose DeepCPI, a novel general and scalable computational framework that combines effective feature embedding (a technique of representation learning) with powerful deep learning methods to accurately predict CPIs at a large scale. DeepCPI automatically learns the implicit yet expressive low-dimensional features of compounds and proteins from a massive amount of unlabeled data. Evaluations of the measured CPIs in large-scale databases, such as ChEMBL and BindingDB, as well as of the known drug–target interactions from DrugBank, demonstrated the superior predictive performance of DeepCPI. Furthermore, several interactions among small-molecule compounds and three G protein-coupled receptor targets (glucagon-like peptide-1 receptor, glucagon receptor, and vasoactive intestinal peptide receptor) predicted using DeepCPI were experimentally validated. The present study suggests that DeepCPI is a useful and powerful tool for drug discovery and repositioning. The source code of DeepCPI can be downloaded from https://github.com/FangpingWan/DeepCPI.
    Type of Medium: Online Resource
    ISSN: 1672-0229 , 2210-3244
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2233708-8
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
  • 10
    Online Resource
    Online Resource
    Scientific Research Publishing, Inc. ; 2016
    In:  Open Journal of Internal Medicine Vol. 06, No. 02 ( 2016), p. 31-36
    In: Open Journal of Internal Medicine, Scientific Research Publishing, Inc., Vol. 06, No. 02 ( 2016), p. 31-36
    Type of Medium: Online Resource
    ISSN: 2162-5972 , 2162-5980
    Language: Unknown
    Publisher: Scientific Research Publishing, Inc.
    Publication Date: 2016
    detail.hit.zdb_id: 2667306-X
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...